performance measurements
Each table row shows performance measurements for this program with a particular command-line input value N.
| N | CPU secs | Elapsed secs | Memory KB | Code B | ≈ CPU Load |
|---|---|---|---|---|---|
| 10,000 | 0.13 | 0.07 | ? | 777 | 33% 14% 14% 14% 86% 17% 17% 0% |
Read the ↓ make, command line, and program output logs to see how this program was run.
Read benchmark to see what this program should do.
notes
source code
# The Computer Language Benchmarks Game
# http://benchmarksgame.alioth.debian.org/
#
# submitted by Ian Osgood
# modified by Sokolov Yura
# modified by bearophile
# modified by xfm for parallelization
# modified by Justin Peel
from sys import stdin
from collections import defaultdict
from multiprocessing import Pool
def gen_freq(frame) :
global sequence
frequences = defaultdict(int)
if frame != 1:
for ii in range(len(sequence)-frame+1) :
frequences[sequence[ii:ii+frame]] += 1
else:
for nucleo in sequence:
frequences[nucleo] += 1
return frequences
def sort_seq(length):
frequences = gen_freq(length)
n= sum(frequences.values())
l = sorted(list(frequences.items()), reverse=True, key=lambda seq_freq: (seq_freq[1],seq_freq[0]))
return '\n'.join("%s %.3f" % (st, 100.0*fr/n) for st,fr in l)
def find_seq(s):
t = gen_freq(len(s))
return (s,t.get(s,0))
def prepare(f=stdin) :
for line in f:
if line[0] in ">;":
if line[1:3] == "TH":
break
seq = []
app = seq.append
for line in f:
if line[0] in ">;":
break
app( line )
return "".join(seq).upper().replace('\n','')
def init(arg):
global sequence
sequence = arg
def main():
global sequence
sequence = prepare()
p=Pool()
res2 = p.map_async(find_seq,reversed("GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT".split()))
res1 = p.map_async(sort_seq,(1,2))
for s in res1.get() : print (s+'\n')
res2 = reversed([r for r in res2.get()])
print ("\n".join("{1:d}\t{0}".format(*s) for s in res2))
if __name__=='__main__' :
main()
make, command-line, and program output logs
Sun, 23 Apr 2023 09:20:24 GMT MAKE: make[1]: Vstupuje se do adresáře „/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp“ nuitka3 --remove-output knucleotide.nuitka-8.nuitka Nuitka-Options:INFO: Used command line options: --remove-output knucleotide.nuitka-8.nuitka Nuitka-Options:WARNING: You did not specify to follow or include anything but main program. Check options and make sure that is intended. Nuitka:INFO: Starting Python compilation with Nuitka '1.5' on Python '3.10' commercial grade 'not installed'. Nuitka-Plugins:INFO: multiprocessing: Injecting pre-module load code for module 'multiprocessing': Nuitka-Plugins:INFO: multiprocessing: Monkey patching "multiprocessing" load environment. Nuitka-Plugins:INFO: multiprocessing: Injecting post-module load code for module 'multiprocessing': Nuitka-Plugins:INFO: multiprocessing: Monkey patching "multiprocessing" for compiled methods. Nuitka:INFO: Completed Python level compilation and optimization. Nuitka:INFO: Generating source code for C backend compiler. Nuitka:INFO: Running data composer tool for optimal constant value handling. Nuitka:INFO: Running C compilation via Scons. Nuitka-Scons:INFO: Backend C compiler: gcc (gcc). Nuitka-Scons:INFO: Backend linking program with 10 files (no progress information available). Nuitka-Scons:WARNING: You are not using ccache. Nuitka:INFO: Removing build directory 'knucleotide.nuitka-8.nuitka.build'. Nuitka:INFO: Successfully created 'knucleotide.nuitka-8.nuitka.bin'. cp knucleotide.nuitka-8.nuitka.bin knucleotide.nuitka-8.nuitka_run make[1]: Opouští se adresář „/home/dundee/work/pybenchmarks/bencher/tmp/knucleotide/tmp“ 19.08s to complete and log all make actions COMMAND LINE: ./knucleotide.nuitka-8.nuitka_run 0 < knucleotide-input10000.txt PROGRAM OUTPUT: A 30.284 T 29.796 C 20.312 G 19.608 AA 9.212 AT 8.950 TT 8.948 TA 8.936 CA 6.166 CT 6.100 AC 6.086 TC 6.042 AG 6.036 GA 5.968 TG 5.868 GT 5.798 CC 4.140 GC 4.044 CG 3.906 GG 3.798 562 GGT 152 GGTA 15 GGTATT 0 GGTATTTTAATT 0 GGTATTTTAATTTATAGT